18-57588259-C-T

Variant names:

• chr18-57588259-C-T
• rs34779648

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.156 in 152,240 control chromosomes in the GnomAD database, including 2,142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2142 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23756 AN: 152122 Hom.: 2142 Cov.: 33

Gnomad AFR AF: 0.0791

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.151

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23760 AN: 152240 Hom.: 2142 Cov.: 33 AF XY: 0.157 AC XY: 11663 AN XY: 74422

African (AFR) AF: 0.0789 AC: 3280 AN: 41556

American (AMR) AF: 0.172 AC: 2625 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3472

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5186

South Asian (SAS) AF: 0.155 AC: 745 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2322 AN: 10584

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13633 AN: 68006

Other (OTH) AF: 0.148 AC: 313 AN: 2114

Alfa AF: 0.160 Hom.: 278

Bravo AF: 0.147

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.0
DANN	Benign	0.91
PhyloP100		-0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34779648; hg19: chr18-55255491;